To select a region, use the Selection mode () (see Section 2.2.3 for a detailed description of the different modes) and select you region of interest in your mapping, then right-click. You are now presented with the dialog shown in Figure 18.15.
When you choose the Extract from Selection option you are presented by the dialog shown in figure 18.16.
The purpose of this dialog is to let you specify what kind of reads you want to include. Per default all reads are included. The options are:
- Paired status
- Include intact paired reads
- When paired reads are placed within the paired distance specified, they will fall into this category. Per default, these reads are colored in blue.
- Include paired reads from broken pairs
- When a pair is broken, either because only one read in the pair matches, or because the distance or relative orientation is wrong, the reads are placed and colored as single reads, but you can still extract them by checking this box.
- Include single reads
- This will include reads that are marked as single reads (as opposed to paired reads). Note that paired reads that have been broken during assembly are not included in this category. Single reads that come from trimming paired sequence lists are included in this category.
- Match specificity
- Include specific matches
- Reads that only are mapped to one position.
- Include non-specific matches
- Reads that have multiple equally good alignments to the reference. These reads are colored yellow per default.
- Alignment quality
- Include perfectly aligned reads
- Reads where the full read is perfectly aligned to the reference sequence (or consensus sequence for de novo assemblies). Note that at the end of the contig, reads may extend beyond the contig (this is not visible unless you make a selection on the read and observe the position numbering in the status bar). Such reads are not considered perfectly aligned reads because they don't align in their entire length.
- Include reads with less than perfect alignment
- Reads with mismatches, insertions or deletions, or with unaligned nucleotides at the ends (the faded part of a read).
- Spliced status
- Include spliced reads
- Reads that are across an intron.
- Include non spliced reads
- Reads that are not across an intron.
One of the benefits of this is that you can actually use this tool to extract subset of reads from a contig. An example work flow could look like this:
- Select the whole reference sequence
- Right-click and Extract from Selection
- Choose to include only paired matches
- Extract the reads from the new file (see Extract sequences)